Gene expression landscapes driving early life stages of the keystone seagrass Posidonia oceanica

KEY MESSAGE: Gene expression analyses reveal tissue-specific and temporally regulated networks driving Posidonia oceanica development, and identify key hub genes that coordinate root, leaf, and seed maturation. Seagrasses are marine angiosperms that form extensive underwater meadows, providing habitat, stabilising sediments, storing carbon, and protecting coastlines. Posidonia oceanica is the endemic foundation seagrass of the Mediterranean Sea, yet its meadows are rapidly declining. Despite its ecological importance, the molecular basis of P. oceanica development is still poorly understood. Here, we analysed gene expression in roots, leaves, and seeds across four developmental stages, revealing strong tissue-specific patterns and temporally regulated expression dynamics. Leaves exhibited active regulation of photosynthesis-related processes, while roots were enriched in pathways related to carbohydrate metabolism and cell wall biogenesis, supporting primary root growth and anchoring. The seeds retained metabolic activity, with glycolytic enzymes indicating readiness for germination. Temporal analyses identified a major transcriptional shift, with distinct gene sets sequentially activated during early establishment and late maturation in tissues. Weighted Gene Co-expression Network Analysis (WGCNA) identified modules strongly associated with specific tissues and developmental transitions, highlighting key hub genes involved in photosynthesis, metabolism, cell wall remodelling, and protein synthesis. Together, these results reveal complex, temporally coordinated regulatory networks underlying P. oceanica development.